Query gi|254780320|ref|YP_003064733.1| translation initiation factor IF-3 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 136 No_of_seqs 113 out of 1373 Neff 5.6 Searched_HMMs 39220 Date Sun May 29 15:41:50 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780320.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG0290 InfC Translation initi 100.0 0 0 359.6 13.3 136 1-136 40-175 (176) 2 CHL00199 infC translation init 100.0 0 0 357.5 15.0 136 1-136 46-181 (182) 3 PRK00028 infC translation init 100.0 0 0 337.1 15.0 135 1-135 39-173 (175) 4 TIGR00168 infC translation ini 100.0 3.4E-30 8.6E-35 201.1 10.3 135 1-135 29-164 (165) 5 pfam00707 IF3_C Translation in 100.0 5E-30 1.3E-34 200.1 9.9 87 48-134 1-87 (87) 6 pfam05198 IF3_N Translation in 99.7 1.9E-17 4.9E-22 125.0 4.5 43 1-43 34-76 (76) 7 pfam06152 Phage_min_cap2 Phage 56.2 7.1 0.00018 20.3 1.8 25 2-26 217-242 (361) 8 COG5014 Predicted Fe-S oxidore 45.4 10 0.00026 19.4 1.2 96 1-115 84-214 (228) 9 cd01226 PH_exo84 Exocyst compl 43.7 10 0.00026 19.4 0.9 21 8-28 5-25 (100) 10 PRK13210 putative L-xylulose 5 41.7 31 0.0008 16.5 6.6 108 1-114 22-139 (284) 11 TIGR02712 urea_carbox urea car 41.0 24 0.00062 17.1 2.6 73 12-86 383-462 (1226) 12 KOG1708 consensus 37.5 13 0.00033 18.8 0.7 82 12-99 94-179 (236) 13 pfam11325 DUF3127 Protein of u 30.2 34 0.00086 16.3 1.9 36 52-94 36-71 (84) 14 TIGR01016 sucCoAbeta succinyl- 27.7 53 0.0014 15.1 2.6 25 80-107 341-365 (389) 15 TIGR02362 dhaK1b probable dihy 26.8 56 0.0014 15.0 2.8 48 69-133 84-131 (328) 16 TIGR01266 fum_ac_acetase fumar 26.6 33 0.00085 16.3 1.3 27 63-89 390-416 (436) 17 KOG4270 consensus 26.5 56 0.0014 14.9 2.7 34 101-134 274-307 (577) 18 PRK07508 para-aminobenzoate sy 25.7 58 0.0015 14.9 5.2 52 54-108 102-155 (377) 19 TIGR00888 guaA_Nterm GMP synth 24.7 47 0.0012 15.4 1.8 26 86-112 168-193 (195) 20 cd03068 PDI_b_ERp72 PDIb famil 24.1 62 0.0016 14.7 5.0 41 68-112 7-47 (107) 21 KOG0238 consensus 23.9 63 0.0016 14.7 3.0 76 13-96 374-454 (670) 22 pfam02679 ComA (2R)-phospho-3- 23.9 63 0.0016 14.7 7.5 97 1-111 91-197 (245) 23 TIGR00827 EIIC-GAT PTS system, 22.0 37 0.00094 16.0 0.8 17 69-93 267-283 (407) 24 pfam05763 DUF835 Protein of un 21.6 70 0.0018 14.4 5.2 67 59-134 54-121 (136) 25 cd04375 RhoGAP_DLC1 RhoGAP_DLC 21.5 70 0.0018 14.4 2.5 39 96-134 123-161 (220) 26 PRK03363 fixB putative electro 21.5 39 0.00099 15.9 0.8 23 89-112 201-223 (313) 27 TIGR02062 RNase_B exoribonucle 21.1 53 0.0013 15.1 1.5 35 78-112 56-92 (664) 28 COG3967 DltE Short-chain dehyd 20.8 23 0.00059 17.3 -0.4 19 67-85 17-35 (245) No 1 >COG0290 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=359.59 Aligned_cols=136 Identities=49% Similarity=0.842 Sum_probs=133.9 Q ss_pred CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCC Q ss_conf 93378579949999887558779998457888888765432110022222002689740086799999999999960379 Q gi|254780320|r 1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGC 80 (136) Q Consensus 1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~ 80 (136) |++|++.|||||+|||+|+||||||||||||+||++|+++|+|++|+.+++|||+|+|+||+|||++|++++++||++|| T Consensus 40 L~lA~e~~LDLV~Ispna~PPVcKImDYGKfkye~~KK~kEakKkQk~i~vKEik~rp~Id~hD~~~K~k~~~rFLe~Gd 119 (176) T COG0290 40 LKLAEEAGLDLVEISPNAKPPVCKIMDYGKFKYEQKKKAKEAKKKQKQIQVKEIKLRPKIDEHDYETKLKNARRFLEKGD 119 (176) T ss_pred HHHHHHCCCCEEEECCCCCCCEEEEEECCCHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHCCC T ss_conf 99999759988998689999844862052067888888887762574577789996157573308999999999987698 Q ss_pred CEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEECCC Q ss_conf 19999997097435735689999999998422432036773248769999920469 Q gi|254780320|r 81 KVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSSKCV 136 (136) Q Consensus 81 kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pkkv 136 (136) +|||+|+|||||++|+|+|..+|++|.++++++|++|++|+++||+|+|+|+|++. T Consensus 120 kVKvtirfrGRe~~h~elG~~vl~r~~~~~~~~~~ve~~pk~egr~m~m~laPkk~ 175 (176) T COG0290 120 KVKVTIRFRGREMAHQELGVKVLERVAEDLEDIAKVESEPKMEGRQMIMVLAPKKK 175 (176) T ss_pred EEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHEEECCCCCCCCEEEEEECCCCC T ss_conf 59999998155560699999999999998654415512601178658999744668 No 2 >CHL00199 infC translation initiation factor 3; Provisional Probab=100.00 E-value=0 Score=357.46 Aligned_cols=136 Identities=44% Similarity=0.684 Sum_probs=134.5 Q ss_pred CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCC Q ss_conf 93378579949999887558779998457888888765432110022222002689740086799999999999960379 Q gi|254780320|r 1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGC 80 (136) Q Consensus 1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~ 80 (136) |++|+++|||||||||+|+||||||||||||+||++|++++++++|+.+++|||+|+|+|++|||++|+++|++||++|| T Consensus 46 l~~A~~~gLDLVevsp~a~PPVcKimDygK~~Ye~~Kk~k~~kkkq~~~~~KEir~~~~I~~hDl~~K~k~a~~FL~~G~ 125 (182) T CHL00199 46 LQLAKKQGLDLVLVSEKSDPPVCRIIDYGKYKFEQEKKAKEAKKKQHNSSIKEVKMRYKIEEHDYQVRINQAFKFLKAGD 125 (182) T ss_pred HHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHCCC T ss_conf 99999849988998899999878986556689999988776440467426666898756576389999999999986799 Q ss_pred CEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEECCC Q ss_conf 19999997097435735689999999998422432036773248769999920469 Q gi|254780320|r 81 KVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSSKCV 136 (136) Q Consensus 81 kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pkkv 136 (136) +|+|+|+|||||++|+|+|.++|++|+++|+++|.+|++|+++||+|+|+|+|+|+ T Consensus 126 kVKv~v~frGRE~~h~e~G~~ll~~~~~~l~~~~~ve~~pk~eGr~~~miL~PkK~ 181 (182) T CHL00199 126 KVKATLTFRGREIQHLSLAINLLNKMAADLSSIAEIQQPPSRDGRNMIMILSPKKV 181 (182) T ss_pred EEEEEEEEECHHHCCHHHHHHHHHHHHHHHHHHEEECCCCCCCCCEEEEEEECCCC T ss_conf 69999998154432689999999999998541378604760008869999924757 No 3 >PRK00028 infC translation initiation factor IF-3; Reviewed Probab=100.00 E-value=0 Score=337.10 Aligned_cols=135 Identities=53% Similarity=0.866 Sum_probs=133.3 Q ss_pred CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCC Q ss_conf 93378579949999887558779998457888888765432110022222002689740086799999999999960379 Q gi|254780320|r 1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGC 80 (136) Q Consensus 1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~ 80 (136) |++|++.|||||+|||+++||||||||||||+|+++|+.++++++|+.+++|||+|+|+||+|||++|++++++||++|| T Consensus 39 l~~A~~~~LDLV~vs~~~~PPVcKi~dygK~~ye~~kk~k~~kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~ 118 (175) T PRK00028 39 LRLAEEAGLDLVEISPNAKPPVCKIMDYGKFKYEQQKKAKEAKKKQKVIEVKEIKLRPKIDEHDYQVKLKNARRFLEKGD 118 (175) T ss_pred HHHHHHCCCCEEEECCCCCCCEEEEEHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCCC T ss_conf 99999819948998789999868985077899999988877652146532003578657560299999999999997799 Q ss_pred CEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEECC Q ss_conf 1999999709743573568999999999842243203677324876999992046 Q gi|254780320|r 81 KVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSSKC 135 (136) Q Consensus 81 kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pkk 135 (136) +|+|+|+|||||++|+|+|.++|++|+++|+++|++|++|+++|++|+|+|+|+| T Consensus 119 kVki~v~~rGRe~~~~e~g~~ll~~~~~~l~~i~~~e~~pk~~Gr~~~~~l~P~k 173 (175) T PRK00028 119 KVKVTIRFRGREIAHKELGMELLERFAEDLEDIAKVEQEPKMEGRQMIMVLAPKK 173 (175) T ss_pred EEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHEEECCCCCCCCCEEEEEEECCC T ss_conf 7999999877556588999999999999722245851477544875999991179 No 4 >TIGR00168 infC translation initiation factor IF-3; InterPro: IPR001288 Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit . The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 . ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation. Probab=99.97 E-value=3.4e-30 Score=201.06 Aligned_cols=135 Identities=45% Similarity=0.788 Sum_probs=132.5 Q ss_pred CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCC Q ss_conf 93378579949999887558779998457888888765432110022222002689740086799999999999960379 Q gi|254780320|r 1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGC 80 (136) Q Consensus 1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~ 80 (136) +.+|.+.+||||+++|++.||||+++|||+|.|++.++.++++++++...+||++++|.|+.||++++++++..|+++|+ T Consensus 29 ~~~~~~~~~dl~~~~~~~~pp~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~g~ 108 (165) T TIGR00168 29 LELAEEAGLDLVLVSPNAKPPVCKLLDYGKYKYEQEKKAKEAKKNQKVIELKEVKLRPTIDEHDLEFKLKNALGFLEKGD 108 (165) T ss_pred HHHHHHCCCCEEEECCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHEEECCCCCCCHHHHHHHHHHHHHHCCC T ss_conf 76664316525763377887532211021023344555665543100111111001133221023456787777763587 Q ss_pred CEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCEEEEEEEECC Q ss_conf 1999999709743573568999999999842243203677-324876999992046 Q gi|254780320|r 81 KVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEP-KFEGRQMIMILSSKC 135 (136) Q Consensus 81 kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~p-k~~Gr~~~~~l~Pkk 135 (136) +++++++|+||+.+|.+.|..+++++...+.+++.++..| +.+|+.+.+++.|++ T Consensus 109 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~p~~ 164 (165) T TIGR00168 109 KVKFTVRFRGRELTHSELGLDVLDRFLEDLADLAEVEKPPTKLEGRSLFLLLAPKK 164 (165) T ss_pred EEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCC T ss_conf 04788763230345778889999999987666654322110110102334430346 No 5 >pfam00707 IF3_C Translation initiation factor IF-3, C-terminal domain. Probab=99.96 E-value=5e-30 Score=200.05 Aligned_cols=87 Identities=52% Similarity=0.866 Sum_probs=85.1 Q ss_pred CCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEE Q ss_conf 22200268974008679999999999996037919999997097435735689999999998422432036773248769 Q gi|254780320|r 48 STGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGCKVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQM 127 (136) Q Consensus 48 ~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~ 127 (136) .+++|||||+|+||+|||++|+++|++||++||+||++|+|||||++|+|.|.++|++|+++++++|.+|++|+++||+| T Consensus 1 ~v~~KEir~~~~I~~hDl~~K~k~a~~FL~~G~kVKv~i~frGRE~~~~e~g~~~l~~i~~~l~~~~~ve~~pk~eGr~~ 80 (87) T pfam00707 1 VVQVKEIKLRPKIDEHDLEVKLKHARKFLEKGDKVKVTIRFRGREIAHPELGRELLDRFAEDLEDIATVEKPPKMEGRNM 80 (87) T ss_pred CEEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHEEECCCCCCCCCEE T ss_conf 95778999726877015999999999999779949999998487565889999999999998551537515876548759 Q ss_pred EEEEEEC Q ss_conf 9999204 Q gi|254780320|r 128 IMILSSK 134 (136) Q Consensus 128 ~~~l~Pk 134 (136) +|+|+|+ T Consensus 81 ~~~l~Pk 87 (87) T pfam00707 81 TMILAPK 87 (87) T ss_pred EEEEECC T ss_conf 9999369 No 6 >pfam05198 IF3_N Translation initiation factor IF-3, N-terminal domain. Probab=99.69 E-value=1.9e-17 Score=125.01 Aligned_cols=43 Identities=49% Similarity=0.828 Sum_probs=40.7 Q ss_pred CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHHHHHHH Q ss_conf 9337857994999988755877999845788888876543211 Q gi|254780320|r 1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKNAVEAR 43 (136) Q Consensus 1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~K 43 (136) |++|++.|||||+|||+++||||||||||||+|+++|+.+++| T Consensus 34 l~~A~~~~LDLV~vs~~a~PPVcki~DygK~~ye~~kk~ke~k 76 (76) T pfam05198 34 LRLAEEKGLDLVEISPNADPPVCKIMDYGKFKYEQQKKAKEAK 76 (76) T ss_pred HHHHHHCCCCEEEECCCCCCCEEEEEECCHHHHHHHHHHHHCC T ss_conf 9999984996899899999988899627118999998786519 No 7 >pfam06152 Phage_min_cap2 Phage minor capsid protein 2. Family of related phage minor capsid proteins. Probab=56.21 E-value=7.1 Score=20.32 Aligned_cols=25 Identities=24% Similarity=0.418 Sum_probs=18.1 Q ss_pred HHHHHCCCCEEEECCCCCC-CEEEEE Q ss_conf 3378579949999887558-779998 Q gi|254780320|r 2 QMAQEANLDLVEIDSSVTP-SVCKIL 26 (136) Q Consensus 2 ~~A~~~~lDLV~vs~~~~P-PVcKi~ 26 (136) +.+++.|.|||+||..+.+ |-|-.. T Consensus 217 ~~~~e~g~d~v~vS~H~garp~capw 242 (361) T pfam06152 217 KRMEEYGVDLVVVSSHAGARPACAPI 242 (361) T ss_pred HHHHHCCCCEEEECCCCCCCCCCCCC T ss_conf 67998198089970787889887770 No 8 >COG5014 Predicted Fe-S oxidoreductase [General function prediction only] Probab=45.36 E-value=10 Score=19.39 Aligned_cols=96 Identities=17% Similarity=0.272 Sum_probs=50.9 Q ss_pred CHHHHHCCCCEEEECCCCCCCEEEEEEHHHHHHHHHHH-----------------------HHHHHHCCCCCCCEEEEEE Q ss_conf 93378579949999887558779998457888888765-----------------------4321100222220026897 Q gi|254780320|r 1 MQMAQEANLDLVEIDSSVTPSVCKILDLRKLRYTIQKN-----------------------AVEARKKQKSTGIKEVKMR 57 (136) Q Consensus 1 l~~A~~~~lDLV~vs~~~~PPVcKi~dygK~~ye~~Kk-----------------------~k~~Kkkq~~~~~KEir~~ 57 (136) +++|++.|.|+|-|| +++|-+|+ .+.-|.--- +-.++-+ --+|.+ T Consensus 84 ~ei~K~~g~d~vRiS-G~EP~l~~-----EHvlevIeLl~~~tFvlETNG~~~g~drslv~el~nr~n------v~vRVs 151 (228) T COG5014 84 LEISKKRGCDLVRIS-GAEPILGR-----EHVLEVIELLVNNTFVLETNGLMFGFDRSLVDELVNRLN------VLVRVS 151 (228) T ss_pred HHHHHHCCCCEEEEE-CCCCCCCH-----HHHHHHHHHCCCCEEEEEECCEEEECCHHHHHHHHCCCC------EEEEEE T ss_conf 999885588689962-89864468-----999999986347649997577688358889999713786------399998 Q ss_pred EE------------CCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 40------------08679999999999996037919999997097435735689999999998422432 Q gi|254780320|r 58 PV------------IDLHDLQVKLKAIDGFLRDGCKVKISVKFRGREIMHQDLGRELLSNIKERFGEISR 115 (136) Q Consensus 58 ~~------------I~~hDl~~K~k~~~~FL~~G~kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~ 115 (136) .+ ....-+...++..+-..++|+++-..+.. + ..+|-+. .++...|+|.+. T Consensus 152 vKG~dpesF~kIT~asp~~F~~QL~aLr~L~~~g~rf~pA~~~-~---f~~Ed~~---k~Lak~Lgehp~ 214 (228) T COG5014 152 VKGWDPESFEKITGASPEYFRYQLKALRHLHGKGHRFWPAVVY-D---FFREDGL---KELAKRLGEHPP 214 (228) T ss_pred ECCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEEEHHHH-C---CCHHHHH---HHHHHHHCCCCC T ss_conf 3579889989875689278999999999998467165101432-0---3513668---999987543899 No 9 >cd01226 PH_exo84 Exocyst complex 84-kDa subunit Pleckstrin Homology (PH) domain. Exo84 is a subunit of the exocyt complex, which is important in intracellular trafficking. In metazoa, Exo84 has a PH domain towards its N-terminus. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes. Probab=43.67 E-value=10 Score=19.41 Aligned_cols=21 Identities=19% Similarity=0.240 Sum_probs=17.9 Q ss_pred CCCEEEECCCCCCCEEEEEEH Q ss_conf 994999988755877999845 Q gi|254780320|r 8 NLDLVEIDSSVTPSVCKILDL 28 (136) Q Consensus 8 ~lDLV~vs~~~~PPVcKi~dy 28 (136) +=||+|++|+..-||||++-| T Consensus 5 ~G~L~ElD~~~~~~i~~v~~f 25 (100) T cd01226 5 YGELEEFDVETKKPVQRVMLF 25 (100) T ss_pred CCCEEEECCCCCCHHHHEEEE T ss_conf 483699767667666621115 No 10 >PRK13210 putative L-xylulose 5-phosphate 3-epimerase; Reviewed Probab=41.73 E-value=31 Score=16.46 Aligned_cols=108 Identities=15% Similarity=0.220 Sum_probs=51.8 Q ss_pred CHHHHHCCCCEEEECCCC-CCCEEEEEEHHHH-HHHHHHHHHHHHHCCCCCCCEEEEEEEE----CCHHHHHHHH---HH Q ss_conf 933785799499998875-5877999845788-8888765432110022222002689740----0867999999---99 Q gi|254780320|r 1 MQMAQEANLDLVEIDSSV-TPSVCKILDLRKL-RYTIQKNAVEARKKQKSTGIKEVKMRPV----IDLHDLQVKL---KA 71 (136) Q Consensus 1 l~~A~~~~lDLV~vs~~~-~PPVcKi~dygK~-~ye~~Kk~k~~Kkkq~~~~~KEir~~~~----I~~hDl~~K~---k~ 71 (136) +++|++.|+|.||+|-+- +..+.++ |+++. +.+..+.. ....+.+-.+-++.. .+..|-.++- .. T Consensus 22 f~~Ak~~Gfd~IE~siDe~d~~~~~l-~~~~~~~~~i~~~~-----~~~gl~I~s~~~s~~~~~pl~s~d~~~r~~~le~ 95 (284) T PRK13210 22 LVLAKECGFDFVEMSVDETDERLARL-DWSKEERLELVKAI-----YETGVRIPSMCLSAHRRFPFGSRDEATRERALEI 95 (284) T ss_pred HHHHHHCCCCEEEEECCCCCCCCCCC-CCCHHHHHHHHHHH-----HHCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHH T ss_conf 99999869988999606754222578-99989999999999-----9829835664155666899999898999999999 Q ss_pred HHHHHCCCCCEEEEE-EECCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 999960379199999-9709743573568999999999842243 Q gi|254780320|r 72 IDGFLRDGCKVKISV-KFRGREIMHQDLGRELLSNIKERFGEIS 114 (136) Q Consensus 72 ~~~FL~~G~kVki~i-~frGRe~~~~e~g~~~l~~i~~~l~~~~ 114 (136) +++.++-..+.-+.+ .+-|-...+.+.-.+..+++++.+..++ T Consensus 96 l~kaI~lA~~LGi~~I~l~g~dv~~~~~~~~~~~rf~e~l~~~~ 139 (284) T PRK13210 96 MKKAIRLAQDLGIRTIQLAGYDVYYEEKDEETRQRFIEGLAWAV 139 (284) T ss_pred HHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 99999999980997899688766668698899999999999999 No 11 >TIGR02712 urea_carbox urea carboxylase; InterPro: IPR014084 Members of this family are ATP-dependent urea carboxylases, including characterised members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae (Baker's yeast). The allophanate hydrolase domain of the yeast enzyme is not included in this entry and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from O. sagaranensis was shown to be highly active on acetamide and formamide as well as urea.. Probab=41.01 E-value=24 Score=17.13 Aligned_cols=73 Identities=15% Similarity=0.229 Sum_probs=44.4 Q ss_pred EEECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCC----CC---CEEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEE Q ss_conf 9998875587799984578888887654321100222----22---0026897400867999999999999603791999 Q gi|254780320|r 12 VEIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKS----TG---IKEVKMRPVIDLHDLQVKLKAIDGFLRDGCKVKI 84 (136) Q Consensus 12 V~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~----~~---~KEir~~~~I~~hDl~~K~k~~~~FL~~G~kVki 84 (136) .+|||.=+|-++||+-||+-|-+.-.+..+|=...+. |. +|.|-.+..-......|++ +..|--..+.|+| T Consensus 383 tevsp~YDPmlAKiIv~g~~R~~A~~kL~~AL~~T~v~Gi~TNLdYLr~i~~s~~F~~g~~sT~~--L~~~~y~~~~iEv 460 (1226) T TIGR02712 383 TEVSPEYDPMLAKIIVHGKDREDAIAKLSQALDETRVYGIETNLDYLRSILSSEVFRSGQVSTRL--LNSFVYTPPAIEV 460 (1226) T ss_pred CEECCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCEEEEECHHHHHHHHCCHHHHHHHHHHHH--HCCCCCCCCEEEE T ss_conf 35677658742446643679789999999887301012354247899988401334102577664--0053546765788 Q ss_pred EE Q ss_conf 99 Q gi|254780320|r 85 SV 86 (136) Q Consensus 85 ~i 86 (136) .. T Consensus 461 ~~ 462 (1226) T TIGR02712 461 LE 462 (1226) T ss_pred EC T ss_conf 64 No 12 >KOG1708 consensus Probab=37.51 E-value=13 Score=18.79 Aligned_cols=82 Identities=24% Similarity=0.151 Sum_probs=45.4 Q ss_pred EEECCCCCCCEEEEEEHHHHHHHHHHHHHHHH----HCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEE Q ss_conf 99988755877999845788888876543211----00222220026897400867999999999999603791999999 Q gi|254780320|r 12 VEIDSSVTPSVCKILDLRKLRYTIQKNAVEAR----KKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGCKVKISVK 87 (136) Q Consensus 12 V~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~K----kkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~kVki~i~ 87 (136) +.|.++.+--|.+=++ -||+|.-..++-+-. .-+.-..-|++.+- |.+|.+. ..---+|+++|-+|+++++ T Consensus 94 tqv~r~~s~VvV~gln-~k~r~~gsekeg~pgtivk~EaPlhvsk~VmLv---dp~d~q~-te~~wr~~e~GekVRvstr 168 (236) T KOG1708 94 TQVIRHRSWVVVKGLN-TKYRHMGSEKEGEPGTIVKSEAPLHVSKQVMLV---DPEDDQP-TEVEWRFTEDGEKVRVSTR 168 (236) T ss_pred EEEEECCCEEEECCCC-HHHHHHCCCCCCCCCEEEEECCCCEEECCEEEE---CCCCCCC-CEEEEEECCCCCEEEEEEC T ss_conf 9986047648972610-344442640028886277503772340406987---7323677-3201577478857999830 Q ss_pred ECCCCCCCHHHH Q ss_conf 709743573568 Q gi|254780320|r 88 FRGREIMHQDLG 99 (136) Q Consensus 88 frGRe~~~~e~g 99 (136) -||.+..+|.. T Consensus 169 -SG~iIpipe~~ 179 (236) T KOG1708 169 -SGRIIPIPEKW 179 (236) T ss_pred -CCCCCCCCCCC T ss_conf -55161475535 No 13 >pfam11325 DUF3127 Protein of unknown function (DUF3127). This bacterial family of proteins has no known function. Probab=30.22 E-value=34 Score=16.26 Aligned_cols=36 Identities=31% Similarity=0.285 Sum_probs=24.4 Q ss_pred EEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCC Q ss_conf 0268974008679999999999996037919999997097435 Q gi|254780320|r 52 KEVKMRPVIDLHDLQVKLKAIDGFLRDGCKVKISVKFRGREIM 94 (136) Q Consensus 52 KEir~~~~I~~hDl~~K~k~~~~FL~~G~kVki~i~frGRe~~ 94 (136) ..|.|...=|.-|+-.. +.-|+.|+|+...+|||-. T Consensus 36 ~~i~fe~~~dk~~~~~~-------~~vGd~V~V~fnl~gREw~ 71 (84) T pfam11325 36 QKICFEFWGDKIDLLDS-------LNVGDEVKVSFDLEGREWN 71 (84) T ss_pred CEEEEEEECCCHHHHCC-------CCCCCEEEEEEEEECCEEC T ss_conf 73899998367567706-------8999989999982536815 No 14 >TIGR01016 sucCoAbeta succinyl-CoA synthetase, beta subunit; InterPro: IPR005809 There are four different enzymes that share a similar catalytic mechanism which involves the phosphorylation by ATP (or GTP) of a specific histidine residue in the active site. These enzymes are: ATP citrate-lyase (4.1.3.8 from EC) , the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues, catalyzes the formation of acetyl-CoA and oxaloacetate from citrate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. ATP-citrate lyase is a tetramer of identical subunits; Succinyl-CoA ligase (GDP-forming) (6.2.1.4 from EC) is a mitochondrial enzyme that catalyzes the substrate level phosphorylation step of the tricarboxylic acid cycle: the formation of succinyl-CoA from succinate with a concomitant hydrolysis of GTP to GDP and phosphate. This enzyme is a dimer composed of an alpha and a beta subunits; Succinyl-CoA ligase (ADP-forming) (6.2.1.5 from EC) is a bacterial enzyme that during aerobic metabolism functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP. It can also function in the other direction for anabolic purposes. This enzyme is a tetramer composed of two alpha and two beta subunits; and Malate-CoA ligase (6.2.1.9 from EC) (malyl-CoA synthetase) , is a bacterial enzyme that forms malyl-CoA from malate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. Malate-CoA ligase is composed of two different subunits. This entry corresponds to a conserved region located in the first half of ATP citrate lyase and in the beta subunits of succinyl-CoA ligases and malate-CoA ligase. ; GO: 0003824 catalytic activity, 0008152 metabolic process. Probab=27.72 E-value=53 Score=15.08 Aligned_cols=25 Identities=20% Similarity=0.472 Sum_probs=16.0 Q ss_pred CCEEEEEEECCCCCCCHHHHHHHHHHHH Q ss_conf 9199999970974357356899999999 Q gi|254780320|r 80 CKVKISVKFRGREIMHQDLGRELLSNIK 107 (136) Q Consensus 80 ~kVki~i~frGRe~~~~e~g~~~l~~i~ 107 (136) -+|.++||+-| ++.|.|+++|...- T Consensus 341 ~~VP~VvRL~G---TN~E~G~~iL~e~g 365 (389) T TIGR01016 341 VNVPVVVRLEG---TNVEEGKKILQESG 365 (389) T ss_pred CCCCEEEECCC---CCHHHHHHHHHHHC T ss_conf 53687898157---88788889999727 No 15 >TIGR02362 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit; InterPro: IPR012735 Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated 2.7.1.29 from EC. By contract, Escherichia coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex.. Probab=26.79 E-value=56 Score=14.98 Aligned_cols=48 Identities=21% Similarity=0.256 Sum_probs=34.7 Q ss_pred HHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEE Q ss_conf 99999996037919999997097435735689999999998422432036773248769999920 Q gi|254780320|r 69 LKAIDGFLRDGCKVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSS 133 (136) Q Consensus 69 ~k~~~~FL~~G~kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~P 133 (136) +=.+.+|+++|..|=+.|+ .|..||++...-+...+.||++.--+++- T Consensus 84 il~~~r~~~~gkGVf~IiK-----------------NF~AD~~~F~~A~~qar~EG~~~~~~iv~ 131 (328) T TIGR02362 84 ILEAIRQVDRGKGVFVIIK-----------------NFEADLSEFSQAIEQARQEGRDIKYIIVH 131 (328) T ss_pred HHHHHHHHHCCCEEEEEEE-----------------CCHHHHHHHHHHHHHHHHCCCCEEEEEEC T ss_conf 9999987524976899971-----------------76777899999999998638950379972 No 16 >TIGR01266 fum_ac_acetase fumarylacetoacetase; InterPro: IPR005959 Fumarylacetoacetase (3.7.1.2 from EC; also known as fumarylacetoacetate hydrolase or FAH) catalyses the hydrolytic cleavage of a carbon-carbon bond in fumarylacetoacetate to yield fumarate and acetoacetate as the final step in phenylalanine and tyrosine degradation . This is an essential metabolic function in humans, the lack of FAH causing type I tyrosinaemia, which is associated with liver and kidney abnormalities and neurological disorders , . The enzyme mechanism involves a catalytic metal ion, a Glu/His catalytic dyad, and a charged oxyanion hole . FAH folds into two domains: an N-terminal domain SH3-like beta-barrel, and a C-terminal with an unusual fold consisting of three layers of beta-sheet structures .; GO: 0004334 fumarylacetoacetase activity, 0009072 aromatic amino acid family metabolic process. Probab=26.61 E-value=33 Score=16.32 Aligned_cols=27 Identities=19% Similarity=0.236 Sum_probs=18.6 Q ss_pred HHHHHHHHHHHHHHCCCCCEEEEEEEC Q ss_conf 799999999999960379199999970 Q gi|254780320|r 63 HDLQVKLKAIDGFLRDGCKVKISVKFR 89 (136) Q Consensus 63 hDl~~K~k~~~~FL~~G~kVki~i~fr 89 (136) +..++=--+.|+||+|||-|-++=+.. T Consensus 390 ~~v~la~g~~R~FL~DGDeVil~g~c~ 416 (436) T TIGR01266 390 KPVKLADGETRKFLEDGDEVILRGVCK 416 (436) T ss_pred CCEECCCCCCCCCCCCCCEEEEEEEEC T ss_conf 411137875132002688699987864 No 17 >KOG4270 consensus Probab=26.50 E-value=56 Score=14.95 Aligned_cols=34 Identities=12% Similarity=0.303 Sum_probs=28.7 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEC Q ss_conf 9999999984224320367732487699999204 Q gi|254780320|r 101 ELLSNIKERFGEISRIDCEPKFEGRQMIMILSSK 134 (136) Q Consensus 101 ~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pk 134 (136) .+|+-++..+++++.-+.-+||.-+++-|+++|+ T Consensus 274 slL~yli~flA~v~~~~~vNKMs~~NlAiV~gPN 307 (577) T KOG4270 274 SLLRYLIRFLADVVEKEHVNKMSARNLAIVFGPN 307 (577) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHCEEEECCC T ss_conf 8899999999998887650246611100574577 No 18 >PRK07508 para-aminobenzoate synthase component I; Provisional Probab=25.74 E-value=58 Score=14.87 Aligned_cols=52 Identities=12% Similarity=0.107 Sum_probs=37.2 Q ss_pred EEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEE--EECCCCCCCHHHHHHHHHHHHH Q ss_conf 689740086799999999999960379199999--9709743573568999999999 Q gi|254780320|r 54 VKMRPVIDLHDLQVKLKAIDGFLRDGCKVKISV--KFRGREIMHQDLGRELLSNIKE 108 (136) Q Consensus 54 ir~~~~I~~hDl~~K~k~~~~FL~~G~kVki~i--~frGRe~~~~e~g~~~l~~i~~ 108 (136) ..+.+.++.-||.-++.++++++..|+--.+.+ +|+++-...+ ..++.++.. T Consensus 102 ~~~~~~~~~~~Y~~~v~~ik~~I~~Gd~YQvnlt~~~~~~~~~~p---~~ly~~Lr~ 155 (377) T PRK07508 102 RDPVARWDFADYAARFERLHRHIRAGDCYQANLTFPVDARWEGDP---LALYRALAA 155 (377) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEECCCCH---HHHHHHHHH T ss_conf 688778999999999999999997598899980599998168999---999999822 No 19 >TIGR00888 guaA_Nterm GMP synthase, N-terminal domain; InterPro: IPR004739 The N-terminal region of GMP synthase 6.3.5.2 from EC is recognised by this signature. GMP synthase catalyzes the synthesis of GMP from XMP , .ATP + xanthosine 5'-phosphate + L-glutamine + H(2)O = AMP + diphosphate + GMP + L-glutamate ; GO: 0003922 GMP synthase (glutamine-hydrolyzing) activity, 0005524 ATP binding, 0006177 GMP biosynthetic process. Probab=24.68 E-value=47 Score=15.43 Aligned_cols=26 Identities=35% Similarity=0.616 Sum_probs=20.0 Q ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 997097435735689999999998422 Q gi|254780320|r 86 VKFRGREIMHQDLGRELLSNIKERFGE 112 (136) Q Consensus 86 i~frGRe~~~~e~g~~~l~~i~~~l~~ 112 (136) |.|.- |.+|.+.|.++|.+|+.++.. T Consensus 168 VQFHP-EV~Ht~~G~~~L~NF~~~~C~ 193 (195) T TIGR00888 168 VQFHP-EVTHTEYGKELLKNFVKDVCG 193 (195) T ss_pred EEECC-CEEECHHHHHHHHHHHHHHCC T ss_conf 65178-312153457899988876315 No 20 >cd03068 PDI_b_ERp72 PDIb family, ERp72 subfamily, first redox inactive TRX-like domain b; ERp72 exhibits both disulfide oxidase and reductase functions like PDI, by catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER and acting as isomerases to correct any non-native disulfide bonds. It also displays chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. ERp72 contains three redox-active TRX (a) domains and two redox inactive TRX-like (b) domains. Its molecular structure is a"abb'a', compared to the abb'a' structure of PDI. ERp72 associates with several ER chaperones and folding factors to form complexes in the ER that bind nascent proteins. Similar to PDI, the b domain of ERp72 is likely involved in binding to substrates. Probab=24.14 E-value=62 Score=14.68 Aligned_cols=41 Identities=34% Similarity=0.450 Sum_probs=30.4 Q ss_pred HHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 999999996037919999997097435735689999999998422 Q gi|254780320|r 68 KLKAIDGFLRDGCKVKISVKFRGREIMHQDLGRELLSNIKERFGE 112 (136) Q Consensus 68 K~k~~~~FL~~G~kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~ 112 (136) -++++++||.+|+-|.|+=.|.|-.-. ..+.+.+.++.+.+ T Consensus 7 s~~~~~~fl~d~ddv~VVGfF~~~ds~----~~~~FlkaA~~lRe 47 (107) T cd03068 7 TLKQVQEFLRDGDDVIIIGVFSGEEDP----AYQLYQDAANSLRE 47 (107) T ss_pred HHHHHHHHHCCCCCEEEEEEECCCCCH----HHHHHHHHHHHCCC T ss_conf 099999985378870899998689977----89999999985505 No 21 >KOG0238 consensus Probab=23.93 E-value=63 Score=14.66 Aligned_cols=76 Identities=17% Similarity=0.151 Sum_probs=44.7 Q ss_pred EECCCCCCCEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEE-----E Q ss_conf 99887558779998457888888765432110022222002689740086799999999999960379199999-----9 Q gi|254780320|r 13 EIDSSVTPSVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMRPVIDLHDLQVKLKAIDGFLRDGCKVKISV-----K 87 (136) Q Consensus 13 ~vs~~~~PPVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~~~I~~hDl~~K~k~~~~FL~~G~kVki~i-----~ 87 (136) +||+.-+|.+|||+.||+-+-+.-.+.+.+- -+-.++--+..=||-..+-...+|-...-..++.- . T Consensus 374 ~vs~~YDpmiaKlvvwg~dR~~Al~kl~~aL--------~~~~I~Gv~tnI~~l~~i~~~~~F~~g~V~T~fi~~~~~el 445 (670) T KOG0238 374 EVSIHYDPMIAKLVVWGKDREEALNKLKDAL--------DNYVIRGVPTNIDFLRDIISHPEFAKGNVSTKFIPEHQPEL 445 (670) T ss_pred CCCCCCCCHHEEEEEECCCHHHHHHHHHHHH--------HHCEEECCCCCHHHHHHHHCCHHHHCCCCCCCCCHHCCCCC T ss_conf 4461136500156676487899999999998--------60688467566689998754766632763015340107444 Q ss_pred ECCCCCCCH Q ss_conf 709743573 Q gi|254780320|r 88 FRGREIMHQ 96 (136) Q Consensus 88 frGRe~~~~ 96 (136) |.++...-. T Consensus 446 f~~~~~~~~ 454 (670) T KOG0238 446 FAPESITPA 454 (670) T ss_pred CCCCCCCCH T ss_conf 675235827 No 22 >pfam02679 ComA (2R)-phospho-3-sulfolactate synthase (ComA). In methanobacteria (2R)-phospho-3-sulfolactate synthase (ComA) catalyses the first step of the biosynthesis of coenzyme M from phosphoenolpyruvate (P-enolpyruvate). This novel enzyme catalyses the stereospecific Michael addition of sulfite to P-enolpyruvate, forming L-2-phospho-3-sulfolactate (PSL). It is suggested that the ComA-catalysed reaction is analogous to those reactions catalysed by beta-elimination enzymes that proceed through an enolate intermediate. Probab=23.90 E-value=63 Score=14.66 Aligned_cols=97 Identities=20% Similarity=0.282 Sum_probs=50.9 Q ss_pred CHHHHHCCCCEEEECCCCCC-CEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCEEEEEE--EECCHHHHHHHHHHHHHHHC Q ss_conf 93378579949999887558-7799984578888887654321100222220026897--40086799999999999960 Q gi|254780320|r 1 MQMAQEANLDLVEIDSSVTP-SVCKILDLRKLRYTIQKNAVEARKKQKSTGIKEVKMR--PVIDLHDLQVKLKAIDGFLR 77 (136) Q Consensus 1 l~~A~~~~lDLV~vs~~~~P-PVcKi~dygK~~ye~~Kk~k~~Kkkq~~~~~KEir~~--~~I~~hDl~~K~k~~~~FL~ 77 (136) ++.+++.|+|-||||.++-. | ...+-+.-++.++. --..+=|+--. -.....+.+-.+++++.||+ T Consensus 91 ~~~~~~lGf~~iEiSdg~i~i~-------~~~~~~~I~~~~~~----G~~v~~EvG~K~~~~~~~~~~~~~I~~~~~~Le 159 (245) T pfam02679 91 LRECKELGFDAIEISDGSIELP-------EEERLRLIRKAKKA----GFKVLSEVGKKDPEADSELTPDELIEQIERDLE 159 (245) T ss_pred HHHHHHCCCCEEEECCCCCCCC-------HHHHHHHHHHHHHC----CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 9999986998899568844689-------89999999999978----997966415467543456799999999999997 Q ss_pred CCCCEEEEEEECCCC----CCCH---HHHHHHHHHHHHHHH Q ss_conf 379199999970974----3573---568999999999842 Q gi|254780320|r 78 DGCKVKISVKFRGRE----IMHQ---DLGRELLSNIKERFG 111 (136) Q Consensus 78 ~G~kVki~i~frGRe----~~~~---e~g~~~l~~i~~~l~ 111 (136) .|--- |.+ -+|| -.+. +.-..++++|++.+. T Consensus 160 aGA~~-Vii--EarEsg~~Gi~~~~g~~r~~~i~~I~~~~~ 197 (245) T pfam02679 160 AGADK-VII--EARESGGVGLYDSDGEVRTDLVEEILERLG 197 (245) T ss_pred CCCCE-EEE--ECCCCCCCCCCCCCCCCHHHHHHHHHHHCC T ss_conf 69828-998--510148756508898871889999997388 No 23 >TIGR00827 EIIC-GAT PTS system, galactitol-specific IIC component; InterPro: IPR013853 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The only characterised member of this family of PTS transporters is the Escherichia coli galactitol transporter. Gat family PTS systems typically have 3 components: IIA, IIB and IIC. This family is specific for the IIC component of the PTS Gat family. It contains fewer proteins than IPR004703 from INTERPRO.. Probab=22.02 E-value=37 Score=16.03 Aligned_cols=17 Identities=41% Similarity=0.755 Sum_probs=10.7 Q ss_pred HHHHHHHHCCCCCEEEEEEECCCCC Q ss_conf 9999999603791999999709743 Q gi|254780320|r 69 LKAIDGFLRDGCKVKISVKFRGREI 93 (136) Q Consensus 69 ~k~~~~FL~~G~kVki~i~frGRe~ 93 (136) .++||+||++ +|+|||. T Consensus 267 s~~AR~~lqk--------~FggrE~ 283 (407) T TIGR00827 267 SESAREFLQK--------KFGGREV 283 (407) T ss_pred HHHHHHHHHH--------HHCCEEE T ss_conf 2788999975--------5288058 No 24 >pfam05763 DUF835 Protein of unknown function (DUF835). The members of this archaebacterial protein family are around 250-300 amino acid residues in length. The function of these proteins is not known. Probab=21.59 E-value=70 Score=14.38 Aligned_cols=67 Identities=19% Similarity=0.310 Sum_probs=52.1 Q ss_pred ECCHHHHHHHHHHHHHHHCC-CCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEC Q ss_conf 00867999999999999603-79199999970974357356899999999984224320367732487699999204 Q gi|254780320|r 59 VIDLHDLQVKLKAIDGFLRD-GCKVKISVKFRGREIMHQDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSSK 134 (136) Q Consensus 59 ~I~~hDl~~K~k~~~~FL~~-G~kVki~i~frGRe~~~~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pk 134 (136) .|+..+|..-...+.+||+. |+. +|.+-|=|.---+.|.+-+-+|+..+.|.+.. .|..++..+.|. T Consensus 54 ~i~Pt~L~~l~~~i~~fl~~~~~~---vV~iDglEYLil~NgF~~v~KfL~~lkD~~~~------~~~~lil~~d~~ 121 (136) T pfam05763 54 AISPTNLHKLLDLIARFLKKNGNG---VVLIDGLEYLVLENGFESVAKFLLSLKDYAIL------HNGTLILVVDPE 121 (136) T ss_pred CCCCCCHHHHHHHHHHHHHHCCCC---EEEEECHHHHHHHCCHHHHHHHHHHHHHHHHH------CCCEEEEEECHH T ss_conf 659754599999999999968995---89991478999971879999999997899835------499899997833 No 25 >cd04375 RhoGAP_DLC1 RhoGAP_DLC1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of DLC1-like proteins. DLC1 shows in vitro GAP activity towards RhoA and CDC42. Beside its C-terminal GAP domain, DLC1 also contains a SAM (sterile alpha motif) and a START (StAR-related lipid transfer action) domain. DLC1 has tumor suppressor activity in cell culture. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. Probab=21.52 E-value=70 Score=14.37 Aligned_cols=39 Identities=15% Similarity=0.262 Sum_probs=32.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEC Q ss_conf 356899999999984224320367732487699999204 Q gi|254780320|r 96 QDLGRELLSNIKERFGEISRIDCEPKFEGRQMIMILSSK 134 (136) Q Consensus 96 ~e~g~~~l~~i~~~l~~~~~~e~~pk~~Gr~~~~~l~Pk 134 (136) |+.-+++|..+...|..++.-...-+|.-.++.++++|+ T Consensus 123 P~~n~~~L~~Ll~fL~~V~~~s~~NkMt~~NLAivfaPn 161 (220) T cd04375 123 PDENREVLQTLLYFLSDVAANSQENQMTATNLAVCLAPS 161 (220) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHEEECHH T ss_conf 999999999999999999971764579747711000105 No 26 >PRK03363 fixB putative electron transfer flavoprotein FixB; Provisional Probab=21.48 E-value=39 Score=15.92 Aligned_cols=23 Identities=22% Similarity=0.284 Sum_probs=14.4 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 097435735689999999998422 Q gi|254780320|r 89 RGREIMHQDLGRELLSNIKERFGE 112 (136) Q Consensus 89 rGRe~~~~e~g~~~l~~i~~~l~~ 112 (136) =||-+..+|. ..++..+.+.|.. T Consensus 201 gGRG~~~~e~-~~l~~eLA~~LGa 223 (313) T PRK03363 201 VGRGIGSKEN-IALAEQLCKAIGA 223 (313) T ss_pred CCCCCCCCHH-HHHHHHHHHHHCC T ss_conf 4876578234-7999999998486 No 27 >TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804 This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process. Probab=21.08 E-value=53 Score=15.11 Aligned_cols=35 Identities=17% Similarity=0.229 Sum_probs=26.9 Q ss_pred CCCCEEEEEEE-CCCCCCCHHHH-HHHHHHHHHHHHH Q ss_conf 37919999997-09743573568-9999999998422 Q gi|254780320|r 78 DGCKVKISVKF-RGREIMHQDLG-RELLSNIKERFGE 112 (136) Q Consensus 78 ~G~kVki~i~f-rGRe~~~~e~g-~~~l~~i~~~l~~ 112 (136) .||||..+|.- +-||.+-||.- ...|.||+.-+.. T Consensus 56 HGDki~A~i~~e~drE~AEPe~LiEp~LtRFvgkv~~ 92 (664) T TIGR02062 56 HGDKIVAVIKKEKDREVAEPEELIEPFLTRFVGKVKL 92 (664) T ss_pred CCCEEEEEEEECCCCCCCCCHHHHHHHHCCEEEEEEE T ss_conf 4882799997358712148434310211234777873 No 28 >COG3967 DltE Short-chain dehydrogenase involved in D-alanine esterification of lipoteichoic acid and wall teichoic acid (D-alanine transfer protein) [Cell envelope biogenesis, outer membrane] Probab=20.78 E-value=23 Score=17.26 Aligned_cols=19 Identities=32% Similarity=0.366 Sum_probs=12.7 Q ss_pred HHHHHHHHHHCCCCCEEEE Q ss_conf 9999999996037919999 Q gi|254780320|r 67 VKLKAIDGFLRDGCKVKIS 85 (136) Q Consensus 67 ~K~k~~~~FL~~G~kVki~ 85 (136) +-+.-+++|++-||+|-|. T Consensus 17 IGl~lak~f~elgN~VIi~ 35 (245) T COG3967 17 IGLALAKRFLELGNTVIIC 35 (245) T ss_pred HHHHHHHHHHHHCCEEEEE T ss_conf 6599999999838979996 Done!